分子动力学模拟中非成键相互作用计算的误差估计

高效的非成键相互作用计算对于分子动力学模拟具有核心意义.本文在一个统一的框架下,综述短程相互作用的截断方法、长程静电相互作用的光滑粒子网格Ewald方法和交错网格Ewald方法的误差估计.与传统的误差估计假设体系均匀且无相关性不同,本文介绍的误差估计可以推广到非均匀和有相关性的体系.本文通过具体例子讨论非均匀性和相关性对误差的本质性影响,以及可能的修正方式,并说明误差估计对于提高非成键相互作用的计算精度和速度有重要作用.本文还展示一个针对光滑粒子网格Ewald方法的实用参数优化方法,使得在保证精度的同时选取计算效率近似最优的参数组合成为可能,改善了传统上参数全凭经验选取的局面.

Error estimates for calculating the non-bonded interactions in molecular dynamics simulations

The error estimates play a central role in the high-performance molecular dynamics simulations. In this paper, we review the error estimates of the cut-off methods, the smooth particle mesh Ewald （SPME） method and the staggered mesh Ewald （StME） method under a unified theoretical frame work. Comparing with the previous error estimates that assume the uniformity and uncorrelatedness of the system, our error estimates can be extended to the inhomogeneous and correlated systems. We present examples that demonstrate why the homogeneity and correlation are important to the error estimates. An efficient way that corrects the inhomogeneity error is proved to increase the computational accuracy greatly. We also present a practical parameter optimization algorithm for the SPME method, by which the computational cost is minimized with a controlled accuracy.